Contacts of the helix formed by residues 99 - 111 (chain C) in PDB entry 2VWI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C GLY 4.8 0.9 - - - +
98C GLY* 1.3 75.4 - - - -
100C VAL* 1.3 62.5 - - - +
101C LEU* 3.4 10.9 + - - +
102C ASP* 2.9 49.9 + - - +
103C ILE* 3.4 9.9 + - - +
149C ALA 4.0 1.1 - - - -
150C GLY* 3.7 21.6 + - - -
152C ILE 3.2 11.9 - - - -
153C LEU* 3.9 5.1 - - - +
154C LEU* 4.9 2.7 - - - -
1294C ANP 4.0 12.8 + - - -
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C SER* 1.3 70.1 - - - +
101C LEU* 1.3 58.6 + - - +
103C ILE* 3.2 13.1 + - + +
104C ILE* 3.0 26.8 + - + +
118C LEU* 4.1 19.3 - - + -
126C ILE* 4.0 17.9 - - + -
149C ALA* 3.6 8.5 + - + +
152C ILE* 3.0 40.2 + - + +
154C LEU* 3.9 20.2 - - + -
220C LEU* 3.6 30.3 - - + -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C SER* 3.1 9.3 + - - +
100C VAL* 1.3 74.6 - - - +
102C ASP* 1.3 57.1 + - - +
104C ILE* 3.2 16.4 + - + +
105C LYS* 2.7 64.8 + - + +
148C LYS* 6.2 0.7 - - - +
149C ALA* 3.4 7.5 + - + +
150C GLY* 3.7 28.3 - - - +
219C GLU* 3.8 20.4 - - - +
223C GLY 5.2 3.4 - - - +
1294C ANP 6.1 0.7 - - - +
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PRO* 3.6 29.2 - - + +
233A MET* 3.8 14.3 + - + +
234A LYS* 3.6 31.4 - - - +
237A MET* 5.7 0.3 - - - +
98C GLY* 3.9 0.7 - - - -
99C SER* 2.9 38.0 + - - +
101C LEU* 1.3 76.6 - - - +
103C ILE* 1.3 58.0 + - + +
105C LYS* 3.4 8.2 + - - +
106C HIS* 3.0 27.9 + - - +
1294C ANP 4.6 4.9 + - - -
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Residues in contact with ILE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A PRO* 6.5 0.4 - - + -
97C GLY 5.4 4.7 - - - +
99C SER 3.4 7.8 + - - +
100C VAL* 3.2 13.1 + - + +
102C ASP* 1.3 75.0 - - + +
104C ILE* 1.3 64.1 + - - +
106C HIS* 3.2 8.1 + - - +
107C ILE* 3.1 40.7 + - + +
118C LEU* 4.0 13.9 - - + -
126C ILE* 5.9 3.6 - - + -
154C LEU* 3.4 31.9 - - + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C VAL* 3.0 20.2 + - + +
101C LEU* 3.2 16.1 + - + +
103C ILE* 1.3 76.0 - - - +
105C LYS* 1.3 64.1 + - + +
107C ILE* 3.3 3.5 + - - +
108C VAL* 3.2 27.0 + - + +
117C VAL* 4.0 14.8 - - + -
118C LEU* 4.1 18.6 - - + -
149C ALA* 4.0 13.2 - - + -
219C GLU* 3.5 22.4 - - + +
220C LEU* 3.8 26.0 - - + -
223C GLY* 3.6 33.9 - - - +
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 3.7 17.9 - - + +
101C LEU* 2.7 48.2 + - + +
102C ASP* 3.7 7.6 - - - +
104C ILE* 1.3 75.0 - - + +
106C HIS* 1.3 57.0 + - - +
108C VAL* 4.1 8.1 - - + +
109C ALA* 3.2 28.6 + - - +
223C GLY 5.3 7.7 + - - -
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Residues in contact with HIS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PRO* 3.9 34.0 - - + +
233A MET* 3.4 28.6 - - + +
102C ASP 3.0 17.1 + - - +
103C ILE* 3.2 8.5 + - - +
105C LYS* 1.3 75.0 - - - +
107C ILE* 1.3 60.6 + - + +
109C ALA* 3.5 1.9 + - - +
110C LYS* 3.1 74.0 + - + +
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE* 3.1 22.9 + - + +
104C ILE 3.3 6.5 + - - +
106C HIS* 1.3 78.8 - - + +
108C VAL* 1.3 59.4 + - - +
110C LYS* 3.5 9.3 + - + +
111C GLY 3.1 3.5 + - - -
112C GLU* 3.0 65.5 + - + +
113C HIS* 4.1 4.3 - - + -
117C VAL* 3.9 26.5 - - + +
118C LEU* 3.6 31.0 - - + -
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Residues in contact with VAL 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C ILE* 3.2 27.3 + - + +
105C LYS* 4.1 8.7 - - + +
107C ILE* 1.3 74.5 - - - +
109C ALA* 1.3 61.1 + - - +
111C GLY* 3.0 19.6 + - - -
113C HIS* 3.6 44.3 + - + +
117C VAL* 4.8 6.5 - - + -
222C THR 5.6 0.2 - - - +
223C GLY* 5.0 6.7 - - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A MET* 4.2 19.3 - - + -
105C LYS 3.2 17.9 + - - +
106C HIS* 3.9 4.7 - - - +
107C ILE 3.4 0.2 - - - -
108C VAL* 1.3 78.4 - - - +
110C LYS* 1.3 61.3 + - + +
111C GLY* 3.6 0.3 + - - -
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Residues in contact with LYS 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C HIS* 3.1 59.5 + - + +
107C ILE* 3.6 7.6 - - + +
108C VAL 3.2 0.2 - - - -
109C ALA* 1.3 76.5 - - - +
111C GLY* 1.3 60.3 + - - +
112C GLU* 3.8 36.5 + - - +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ILE 3.1 0.6 + - - -
108C VAL 3.0 16.6 + - - -
109C ALA 3.3 1.0 + - - -
110C LYS* 1.3 80.3 - - - +
112C GLU* 1.3 58.7 + - - +
113C HIS* 3.4 16.6 - - - -
114C LYS* 3.5 24.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il